Coded particles enable formation of positionally flexible arrays for multiplexed analysis of samples and reagents. Such coded particles may include a code portion and an assay portion. The code portion defines an optically detectable code for tracking and identifying each particle in a mixture of particles. The assay portion provides a region for performing an assay and for detecting an optical outcome of the assay. Accordingly, the code and assay portions should not interfere optically with one another. One approach to avoid optical interference is to spatially segregate the code and assay portions, so that each may be detected separately. However, spatial segregation may not be sufficient in some cases, for example, when the code and assay portions have similar optical properties. In addition, spatial segregation may be undesirable because it increases the size of the particles or reduces the space on each particle for performing assays.